Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010771.1 Corchorus olitorius cultivar O-4 contig10803, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 36783
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:3861 original size:17 final size:16
Alignment explanation
Indices: 3835--3868 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3825 AAAAAATGGA
3835 GAGGTGTGAAGAGTGT
1 GAGGTGTGAAGAGTGT
*
3851 GAGGTTGTGAAGGGTGT
1 GAGG-TGTGAAGAGTGT
3868 G
1 G
3869 GGAGGATCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.21, C:0.00, G:0.53, T:0.26
Consensus pattern (16 bp):
GAGGTGTGAAGAGTGT
Found at i:5454 original size:27 final size:27
Alignment explanation
Indices: 5424--5492 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 27
5414 AACTTAAAAC
* * * *
5424 GACCAAAATGTCTCTGAATGTGCATAT
1 GACCAAAATGCCCCTGAACGTGCAAAT
*
5451 GACCAAAATGCCCCTGGACGTGCAAAT
1 GACCAAAATGCCCCTGAACGTGCAAAT
*
5478 GACTAAAATGCCCCT
1 GACCAAAATGCCCCT
5493 AGGTGACCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (27 bp):
GACCAAAATGCCCCTGAACGTGCAAAT
Found at i:7952 original size:10 final size:10
Alignment explanation
Indices: 7892--7944 Score: 53
Period size: 9 Copynumber: 5.7 Consensus size: 10
7882 AGCTGATATT
7892 AAAAA-AATA
1 AAAAATAATA
7901 AAAAATAAT-
1 AAAAATAATA
7910 AAAAAT--TCA
1 AAAAATAAT-A
*
7919 AAAAATTA-A
1 AAAAATAATA
7928 AAAAATAATA
1 AAAAATAATA
7938 AAAAATA
1 AAAAATA
7945 TTTAAAAAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
7 1 0.03
9 25 0.68
10 11 0.30
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAAATAATA
Found at i:11391 original size:50 final size:50
Alignment explanation
Indices: 11246--11395 Score: 169
Period size: 50 Copynumber: 3.0 Consensus size: 50
11236 AAAATGTCTC
** * *
11246 TTGAAAAGCGAATTTTGATCTT-AGACTCACAAATGGACCGCAATCTTACT
1 TTGAAAAGCGAATTTTGATCTTGA-ACTCACAAATGGAAAGCAATTTTATT
** ** *
11296 TTGAAAAGCGAATTTTGATCTTGGGCTCTGACATGGAAAGCAATTTTATT
1 TTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTATT
**
11346 TTGCAAAA-CGAATTTTGATCTTGAACTCACAAATGGAAATAAATTTTATT
1 TTG-AAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTATT
11396 GTAAAAACTT
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
50 78 0.95
51 4 0.05
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (50 bp):
TTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTATT
Found at i:14565 original size:21 final size:22
Alignment explanation
Indices: 14526--14567 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
14516 CTAAGGTTTA
14526 ATGGAATGCATGAACGAATGCC
1 ATGGAATGCATGAACGAATGCC
* *
14548 ATGGCATG-ATGAATGAATGC
1 ATGGAATGCATGAACGAATGC
14568 ATGAAGCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (22 bp):
ATGGAATGCATGAACGAATGCC
Found at i:20712 original size:52 final size:54
Alignment explanation
Indices: 20629--20731 Score: 156
Period size: 52 Copynumber: 1.9 Consensus size: 54
20619 GAGTTTGGTG
20629 GCAAGGCCCATGTGTATAAATTATGAGCCTTTGCCACAAAGAGAAATGCCTTAACA
1 GCAAGGCCCA-GTGTAT-AATTATGAGCCTTTGCCACAAAGAGAAATGCCTTAACA
* *
20685 GCAAGGCCCA-TGTAT-ATTATGAGCCTTTGCCATAAGGAGAAATGCCT
1 GCAAGGCCCAGTGTATAATTATGAGCCTTTGCCACAAAGAGAAATGCCT
20732 CTGTGTTATA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
52 30 0.67
54 5 0.11
56 10 0.22
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (54 bp):
GCAAGGCCCAGTGTATAATTATGAGCCTTTGCCACAAAGAGAAATGCCTTAACA
Found at i:20773 original size:43 final size:42
Alignment explanation
Indices: 20726--21054 Score: 434
Period size: 43 Copynumber: 7.8 Consensus size: 42
20716 ATAAGGAGAA
*
20726 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-AATATAG
* * *
20769 ATGCCCCTGTGTTATATATGTGTTTGGGGAC-TTGAATATAT
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGAATATAG
*
20810 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-AATATAG
*
20853 ATGCC-CTTGTGTTATATATGTGTTTGGGGAC-TTGAATATAG
1 ATGCCTC-TGTGTTATATATGTGTTTGAGGACTTTGAATATAG
*
20894 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAATG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-AATATA-G
* * *
20938 -TGCCCCTGTGTTGTATATATGTTTGAGGACTTTG-ATATAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGAATATAG
*
20978 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTTGGAATAGAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGAC--TTT-GAATATAG
* *
21023 ATGCCCCTGTGTTATATATGTGTTTGGGGACT
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACT
21055 CTTAGTTATT
Statistics
Matches: 252, Mismatches: 22, Indels: 24
0.85 0.07 0.08
Matches are distributed among these distances:
40 1 0.00
41 99 0.39
42 14 0.06
43 102 0.40
44 2 0.01
45 34 0.13
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.42
Consensus pattern (42 bp):
ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGAATATAG
Found at i:20838 original size:84 final size:84
Alignment explanation
Indices: 20726--21054 Score: 536
Period size: 84 Copynumber: 3.9 Consensus size: 84
20716 ATAAGGAGAA
*
20726 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGATGCCCCTGTGTTATATATGTG
*
20791 TTTGGGGACTTGAATATAT
66 TTTGGGGACTTGAATATAG
*
20810 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGATGCCCTTGTGTTATATATGTG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGATGCCCCTGTGTTATATATGTG
20875 TTTGGGGACTTGAATATAG
66 TTTGGGGACTTGAATATAG
* *
20894 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAATG-TGCCCCTGTGTTGTATATAT
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAA-GATGCCCCTGTGTTATATATGT
*
20958 GTTTGAGGACTTTG-ATATAG
65 GTTTGGGGAC-TTGAATATAG
* *
20978 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTTGGAATAGAGATGCCCCTGTGTTATATATG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGAC--TTTGTAATAAAGATGCCCCTGTGTTATATATG
21043 TGTTTGGGGACT
64 TGTTTGGGGACT
21055 CTTAGTTATT
Statistics
Matches: 228, Mismatches: 12, Indels: 9
0.92 0.05 0.04
Matches are distributed among these distances:
84 186 0.82
85 6 0.03
86 36 0.16
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.42
Consensus pattern (84 bp):
ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGATGCCCCTGTGTTATATATGTG
TTTGGGGACTTGAATATAG
Found at i:21935 original size:17 final size:16
Alignment explanation
Indices: 21913--21946 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21903 AAACCTTTAA
*
21913 TTTTAAAACCTAAAAAT
1 TTTTAAAA-ATAAAAAT
21930 TTTTAAAAATAAAAAT
1 TTTTAAAAATAAAAAT
21946 T
1 T
21947 AGCTCAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TTTTAAAAATAAAAAT
Found at i:24393 original size:19 final size:19
Alignment explanation
Indices: 24371--24411 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
24361 CCTCTTTTAA
* *
24371 TTTTTT-GATTTTTTTCCT
1 TTTTTTGGATTTCTGTCCT
24389 TTTTTTGGATTTCTGTCCT
1 TTTTTTGGATTTCTGTCCT
24408 TTTT
1 TTTT
24412 CTATCTCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.05, C:0.12, G:0.10, T:0.73
Consensus pattern (19 bp):
TTTTTTGGATTTCTGTCCT
Found at i:27750 original size:27 final size:27
Alignment explanation
Indices: 27712--27783 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 27
27702 AGTGGACTTT
* *
27712 AAATGACCAAAACGCCCCTAAATGTGC
1 AAATGACCAAAATGCCCCTAAATATGC
* *
27739 AAATGACCAAAATGCCCTTGAATATGC
1 AAATGACCAAAATGCCCCTAAATATGC
27766 AAATGACCAAAATGCCCC
1 AAATGACCAAAATGCCCC
27784 CGGATGACCC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.42, C:0.28, G:0.14, T:0.17
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTAAATATGC
Found at i:31815 original size:2 final size:2
Alignment explanation
Indices: 31808--31836 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31798 CAGATGAGTG
31808 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31837 ATGTTGGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34339 original size:2 final size:2
Alignment explanation
Indices: 34332--34366 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
34322 TTATGATTAT
34332 TA TA TA TA TA -A TA TA TA -A TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34367 CAACCCTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.